+Open data
-Basic information
Entry | Database: PDB / ID: 7wkk | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the IR subunit from X. laevis NPC | ||||||
Components |
| ||||||
Keywords | STRUCTURAL PROTEIN / nuclear pore complex / inner ring / Nup205 / Nup93 / Nup188 / Nup155 / NDC1 / Aladin | ||||||
Function / homology | Function and homology information nuclear pore complex assembly / structural constituent of nuclear pore / nuclear localization sequence binding / mRNA transport / nuclear pore / nuclear periphery / protein transport / nuclear membrane / membrane => GO:0016020 / cytosol Similarity search - Function | ||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Huang, G. / Zhan, X. / Shi, Y. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Cell Res / Year: 2022 Title: Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex. Authors: Gaoxingyu Huang / Xiechao Zhan / Chao Zeng / Ke Liang / Xuechen Zhu / Yanyu Zhao / Pan Wang / Qifan Wang / Qiang Zhou / Qinghua Tao / Minhao Liu / Jianlin Lei / Chuangye Yan / Yigong Shi / Abstract: Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an ...Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7wkk.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7wkk.ent.gz | 1.8 MB | Display | PDB format |
PDBx/mmJSON format | 7wkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/7wkk ftp://data.pdbj.org/pub/pdb/validation_reports/wk/7wkk | HTTPS FTP |
---|
-Related structure data
Related structure data | 32566MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein , 9 types, 30 molecules AaBbCEceDFMdfmGJgjHLhlIKikOoNn
#1: Protein | Mass: 227854.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642R6 #2: Protein | Mass: 195848.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8F1N1 #3: Protein | Mass: 93565.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZX96 #4: Protein | Mass: 154922.422 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q7ZWL0 #5: Protein | Mass: 58618.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: K9ZTJ6 #6: Protein | Mass: 55969.496 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q91349 #7: Protein | Mass: 61216.863 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5EAX5 #8: Protein | Mass: 57120.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6DCM0 #9: Protein | Mass: 74420.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q6AX31 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The IR subunit / Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Xenopus laevis (African clawed frog) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2093631 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 4.2 Å | ||||||||||||||||||||||||
Refine LS restraints |
|